Face normals facing the wrong direction will show up red in Netfabb basic also. Upload your object/stl file here so folks here can get a better look, possibly diagnose the problem.

Ignore the comments about the normals. I had a confusion attack. You have two holes, the inner hemispheres upper edge and the outer surfaces upper edge. Netfab will just close the outer cups edge when you try to repair it,leaving 2 shells. I bet you will wind up having to perform a boolean operartion, or manually connect verts, and fill holes

[Updated on: Thu, 29 November 2012 20:24 UTC]

Have any questions regarding Blender, and need fast answers, you are always welcome at the IRC Server Freenode, channel #blender. As a bonus, several there have experience in modelling for 3D prints.

Export your file to Netfabb.
Click on repair, Red Cross
Hover over the icons at the top till you find 'Add Triangles' Click this
Pick one of the edges. It will turn blue. Pick another face over the red internal part.
A new face will be created.
Right click on the edge of the new face and pick 'Close Hole'.
The internal red is covered by a new face.
Flip model over and do the same on the other side.
Once done. Click on Apply Repair.
Go to Part - Export part.
Export as STL.

I tried out Jacants technique which worked wonderfully. I never did export it as a stl in NF for some reason. Opened it in Blender, some odd reason the holes were filled, except the interior one. Anyone that uses Blender needs to experiment with this, to prove I am not going crazier.

Have any questions regarding Blender, and need fast answers, you are always welcome at the IRC Server Freenode, channel #blender. As a bonus, several there have experience in modelling for 3D prints.